The SIMARINE-NATURA project’s prime objective is to designate marine Natura 2000 sites for the Mediterranean Shag (Phalacrocorax aristotelis desmarestii) in Slovenia. This fisheating sea bird subspecies, which is distributed only in the Mediterranean and Black Seas, is listed in Annex I of the Birds Directive. In the Northern Adriatic, Mediterranean Shags gather in large numbers during the summer and autumn months, as this shallow and fish-rich sea is highly favourable for their sustenance. They roost in large groups at the very edge of the sea. On the Slovenian coast, even more than 2,000 individuals gather at three different roost sites, which is more than one tenth of their population. The nearest breeding sites to Slovenia are situated on the rocky Croatian coast and islands. A large part of the project has been dedicated to the research into the Mediterranean Shag’s distribution and ecology in the Slovenian sea, which will enable identification of the key sites for its protection in our country. It is envisaged that marine Natura 2000 sites will be designated in 2015.